OpenRaiser/Intern-Atlas huggingface dataset:
ClinicalGPT-R1: Pushing reasoning capability of generalist disease diagnosis with large language model
Venue: arXiv cs.CL 2025
Year: 2025

Recent advances in reasoning with large language models (LLMs)has shown remarkable reasoning capabilities in domains such as mathematics and coding, yet their application to clinical diagnosis remains underexplored. Here, we introduce ClinicalGPT-R1, a reasoning enhanced generalist large language model for disease diagnosis. Trained on a dataset of 20,000 real-world clinical records, ClinicalGPT-R1 leverages diverse training strategies to enhance diagnostic reasoning. To benchmark performance, we curated MedBench-Hard, a challenging dataset spanning seven major medical specialties and representative diseases. Experimental results demonstrate that ClinicalGPT-R1 outperforms GPT-4o in Chinese diagnostic tasks and achieves comparable performance to GPT-4 in English settings. This comparative study effectively validates the superior performance of ClinicalGPT-R1 in disease diagnosis tasks. Resources are available at https://github.com/medfound/medfound.
D$^2$iT: Dynamic Diffusion Transformer for Accurate Image Generation
Venue: arXiv cs.CV 2025
Year: 2025

Diffusion models are widely recognized for their ability to generate high-fidelity images. Despite the excellent performance and scalability of the Diffusion Transformer (DiT) architecture, it applies fixed compression across different image regions during the diffusion process, disregarding the naturally varying information densities present in these regions. However, large compression leads to limited local realism, while small compression increases computational complexity and compromises global consistency, ultimately impacting the quality of generated images. To address these limitations, we propose dynamically compressing different image regions by recognizing the importance of different regions, and introduce a novel two-stage framework designed to enhance the effectiveness and efficiency of image generation: (1) Dynamic VAE (DVAE) at first stage employs a hierarchical encoder to encode different image regions at different downsampling rates, tailored to their specific information densities, thereby providing more accurate and natural latent codes for the diffusion process. (2) Dynamic Diffusion Transformer (D$^2$iT) at second stage generates images by predicting multi-grained noise, consisting of coarse-grained (less latent code in smooth regions) and fine-grained (more latent codes in detailed regions), through an novel combination of the Dynamic Grain Transformer and the Dynamic Content Transformer. The strategy of combining rough prediction of noise with detailed regions correction achieves a unification of global consistency and local realism. Comprehensive experiments on various generation tasks validate the effectiveness of our approach. Code will be released at https://github.com/jiawn-creator/Dynamic-DiT.
Measuring Leakage in Concept-Based Methods: An Information Theoretic Approach
Venue: arXiv cs.LG 2025
Year: 2025

Concept Bottleneck Models (CBMs) aim to enhance interpretability by structuring predictions around human-understandable concepts. However, unintended information leakage, where predictive signals bypass the concept bottleneck, compromises their transparency. This paper introduces an information-theoretic measure to quantify leakage in CBMs, capturing the extent to which concept embeddings encode additional, unintended information beyond the specified concepts. We validate the measure through controlled synthetic experiments, demonstrating its effectiveness in detecting leakage trends across various configurations. Our findings highlight that feature and concept dimensionality significantly influence leakage, and that classifier choice impacts measurement stability, with XGBoost emerging as the most reliable estimator. Additionally, preliminary investigations indicate that the measure exhibits the anticipated behavior when applied to soft joint CBMs, suggesting its reliability in leakage quantification beyond fully synthetic settings. While this study rigorously evaluates the measure in controlled synthetic experiments, future work can extend its application to real-world datasets.
Draw with Thought: Unleashing Multimodal Reasoning for Scientific Diagram Generation
Venue: arXiv cs.AI 2025
Year: 2025

Scientific diagrams are vital tools for communicating structured knowledge across disciplines. However, they are often published as static raster images, losing symbolic semantics and limiting reuse. While Multimodal Large Language Models (MLLMs) offer a pathway to bridging vision and structure, existing methods lack semantic control and structural interpretability, especially on complex diagrams. We propose Draw with Thought (DwT), a training-free framework that guides MLLMs to reconstruct diagrams into editable mxGraph XML code through cognitively-grounded Chain-of-Thought reasoning. DwT enables interpretable and controllable outputs without model fine-tuning by dividing the task into two stages: Coarse-to-Fine Planning, which handles perceptual structuring and semantic specification, and Structure-Aware Code Generation, enhanced by format-guided refinement. To support evaluation, we release Plot2XML, a benchmark of 247 real-world scientific diagrams with gold-standard XML annotations. Extensive experiments across eight MLLMs show that our approach yields high-fidelity, semantically aligned, and structurally valid reconstructions, with human evaluations confirming strong alignment in both accuracy and visual aesthetics, offering a scalable solution for converting static visuals into executable representations and advancing machine understanding of scientific graphics.
HalluShift: Measuring Distribution Shifts towards Hallucination Detection in LLMs
Venue: arXiv cs.CL 2025
Year: 2025

Large Language Models (LLMs) have recently garnered widespread attention due to their adeptness at generating innovative responses to the given prompts across a multitude of domains. However, LLMs often suffer from the inherent limitation of hallucinations and generate incorrect information while maintaining well-structured and coherent responses. In this work, we hypothesize that hallucinations stem from the internal dynamics of LLMs. Our observations indicate that, during passage generation, LLMs tend to deviate from factual accuracy in subtle parts of responses, eventually shifting toward misinformation. This phenomenon bears a resemblance to human cognition, where individuals may hallucinate while maintaining logical coherence, embedding uncertainty within minor segments of their speech. To investigate this further, we introduce an innovative approach, HalluShift, designed to analyze the distribution shifts in the internal state space and token probabilities of the LLM-generated responses. Our method attains superior performance compared to existing baselines across various benchmark datasets. Our codebase is available at https://github.com/sharanya-dasgupta001/hallushift.
GenEDA: Towards Generative Netlist Functional Reasoning via Cross-Modal Circuit Encoder-Decoder Alignment
Venue: arXiv cs.LG 2025
Year: 2025

The success of foundation AI has motivated the research of circuit foundation models, which are customized to assist the integrated circuit (IC) design process. However, existing pre-trained circuit foundation models are typically limited to standalone encoders for predictive tasks or decoders for generative tasks. These two model types are developed independently, operate on different circuit modalities, and reside in separate latent spaces. This restricts their ability to complement each other for more advanced capabilities. In this work, we present GenEDA, the first framework that cross-modally aligns circuit encoders with decoders within a shared latent space. GenEDA bridges the gap between graph-based circuit representation learning and text-based large language models (LLMs), enabling communication between their respective latent spaces. To achieve the alignment, we propose two paradigms to support both open-source trainable LLMs and commercial frozen LLMs. We leverage this aligned architecture to develop the first generative foundation model for netlists, unleashing LLMs' generative reasoning capability on the low-level and bit-blasted netlists. GenEDA enables three unprecedented generative netlist functional reasoning tasks, where it reversely generates high-level functionalities such as specifications and RTL code from low-level netlists. These tasks move beyond traditional gate function classification to direct generation of full-circuit functionality. Experiments demonstrate that GenEDA significantly boosts advanced LLMs' (e.g., GPT and DeepSeek series) performance in all tasks.
EasyREG: Easy Depth-Based Markerless Registration and Tracking using Augmented Reality Device for Surgical Guidance
Venue: arXiv cs.CV 2025
Year: 2025

The use of Augmented Reality (AR) devices for surgical guidance has gained increasing traction in the medical field. Traditional registration methods often rely on external fiducial markers to achieve high accuracy and real-time performance. However, these markers introduce cumbersome calibration procedures and can be challenging to deploy in clinical settings. While commercial solutions have attempted real-time markerless tracking using the native RGB cameras of AR devices, their accuracy remains questionable for medical guidance, primarily due to occlusions and significant outliers between the live sensor data and the preoperative target anatomy point cloud derived from MRI or CT scans. In this work, we present a markerless framework that relies only on the depth sensor of AR devices and consists of two modules: a registration module for high-precision, outlier-robust target anatomy localization, and a tracking module for real-time pose estimation. The registration module integrates depth sensor error correction, a human-in-the-loop region filtering technique, and a robust global alignment with curvature-aware feature sampling, followed by local ICP refinement, for markerless alignment of preoperative models with patient anatomy. The tracking module employs a fast and robust registration algorithm that uses the initial pose from the registration module to estimate the target pose in real-time. We comprehensively evaluated the performance of both modules through simulation and real-world measurements. The results indicate that our markerless system achieves superior performance for registration and comparable performance for tracking to industrial solutions. The two-module design makes our system a one-stop solution for surgical procedures where the target anatomy moves or stays static during surgery.
MADLLM: Multivariate Anomaly Detection via Pre-trained LLMs
Venue: arXiv cs.CL 2025
Year: 2025

When applying pre-trained large language models (LLMs) to address anomaly detection tasks, the multivariate time series (MTS) modality of anomaly detection does not align with the text modality of LLMs. Existing methods simply transform the MTS data into multiple univariate time series sequences, which can cause many problems. This paper introduces MADLLM, a novel multivariate anomaly detection method via pre-trained LLMs. We design a new triple encoding technique to align the MTS modality with the text modality of LLMs. Specifically, this technique integrates the traditional patch embedding method with two novel embedding approaches: Skip Embedding, which alters the order of patch processing in traditional methods to help LLMs retain knowledge of previous features, and Feature Embedding, which leverages contrastive learning to allow the model to better understand the correlations between different features. Experimental results demonstrate that our method outperforms state-of-the-art methods in various public anomaly detection datasets.
Capturing Longitudinal Changes in Brain Morphology Using Temporally Parameterized Neural Displacement Fields
Venue: arXiv cs.CV 2025
Year: 2025

Longitudinal image registration enables studying temporal changes in brain morphology which is useful in applications where monitoring the growth or atrophy of specific structures is important. However this task is challenging due to; noise/artifacts in the data and quantifying small anatomical changes between sequential scans. We propose a novel longitudinal registration method that models structural changes using temporally parameterized neural displacement fields. Specifically, we implement an implicit neural representation (INR) using a multi-layer perceptron that serves as a continuous coordinate-based approximation of the deformation field at any time point. In effect, for any N scans of a particular subject, our model takes as input a 3D spatial coordinate location x, y, z and a corresponding temporal representation t and learns to describe the continuous morphology of structures for both observed and unobserved points in time. Furthermore, we leverage the analytic derivatives of the INR to derive a new regularization function that enforces monotonic rate of change in the trajectory of the voxels, which is shown to provide more biologically plausible patterns. We demonstrate the effectiveness of our method on 4D brain MR registration.
A Categorical Unification for Multi-Model Data: Part II Categorical Algebra and Calculus
Venue: arXiv cs.DB 2025
Year: 2025

Multi-model databases are designed to store, manage, and query data in various models, such as relational, hierarchical, and graph data, simultaneously. In this paper, we provide a theoretical basis for querying categorical databases. We propose two formal query languages: categorical calculus and categorical algebra, by extending relational calculus and relational algebra respectively. We demonstrate the equivalence between these two languages of queries. We propose a series of transformation rules of categorical algebra to facilitate query optimization. Finally, we analyze the expressive power and computation complexity for the proposed query languages.
FSSUAVL: A Discriminative Framework using Vision Models for Federated Self-Supervised Audio and Image Understanding
Venue: arXiv cs.SD 2025
Year: 2025

Recent studies have demonstrated that vision models can effectively learn multimodal audio-image representations when paired. However, the challenge of enabling deep models to learn representations from unpaired modalities remains unresolved. This issue is especially pertinent in scenarios like Federated Learning (FL), where data is often decentralized, heterogeneous, and lacks a reliable guarantee of paired data. Previous attempts tackled this issue through the use of auxiliary pretrained encoders or generative models on local clients, which invariably raise computational cost with increasing number modalities. Unlike these approaches, in this paper, we aim to address the task of unpaired audio and image recognition using \texttt{FSSUAVL}, a single deep model pretrained in FL with self-supervised contrastive learning (SSL). Instead of aligning the audio and image modalities, \texttt{FSSUAVL} jointly discriminates them by projecting them into a common embedding space using contrastive SSL. This extends the utility of \texttt{FSSUAVL} to paired and unpaired audio and image recognition tasks. Our experiments with CNN and ViT demonstrate that \texttt{FSSUAVL} significantly improves performance across various image- and audio-based downstream tasks compared to using separate deep models for each modality. Additionally, \texttt{FSSUAVL}'s capacity to learn multimodal feature representations allows for integrating auxiliary information, if available, to enhance recognition accuracy.
BIT: Battery-free, IC-less and Wireless Smart Textile Interface and Sensing System
Venue: arXiv cs.HC 2025
Year: 2025

The development of smart textile interfaces is hindered by the inclusion of rigid hardware components and batteries within the fabric, which pose challenges in terms of manufacturability, usability, and environmental concerns related to electronic waste. To mitigate these issues, we propose a smart textile interface and its wireless sensing system to eliminate the need for ICs, batteries, and connectors embedded into textiles. Our technique is established on the integration of multi-resonant circuits in smart textile interfaces, and utilizing near-field electromagnetic coupling between two coils to facilitate wireless power transfer and data acquisition from smart textile interface. A key aspect of our system is the development of a mathematical model that accurately represents the equivalent circuit of the sensing system. Using this model, we developed a novel algorithm to accurately estimate sensor signals based on changes in system impedance. Through simulation-based experiments and a user study, we demonstrate that our technique effectively supports multiple textile sensors of various types.
LLMs Can Achieve High-quality Simultaneous Machine Translation as Efficiently as Offline
Venue: arXiv cs.CL 2025
Year: 2025

When the complete source sentence is provided, Large Language Models (LLMs) perform excellently in offline machine translation even with a simple prompt "Translate the following sentence from [src lang] into [tgt lang]:". However, in many real scenarios, the source tokens arrive in a streaming manner and simultaneous machine translation (SiMT) is required, then the efficiency and performance of decoder-only LLMs are significantly limited by their auto-regressive nature. To enable LLMs to achieve high-quality SiMT as efficiently as offline translation, we propose a novel paradigm that includes constructing supervised fine-tuning (SFT) data for SiMT, along with new training and inference strategies. To replicate the token input/output stream in SiMT, the source and target tokens are rearranged into an interleaved sequence, separated by special tokens according to varying latency requirements. This enables powerful LLMs to learn read and write operations adaptively, based on varying latency prompts, while still maintaining efficient auto-regressive decoding. Experimental results show that, even with limited SFT data, our approach achieves state-of-the-art performance across various SiMT benchmarks, and preserves the original abilities of offline translation. Moreover, our approach generalizes well to document-level SiMT setting without requiring specific fine-tuning, even beyond the offline translation model.
Outage Probability Analysis for OTFS with Finite Blocklength
Venue: arXiv cs.IR 2025
Year: 2025

Orthogonal time frequency space (OTFS) modulation is widely acknowledged as a prospective waveform for future wireless communication networks.To provide insights for the practical system design, this paper analyzes the outage probability of OTFS modulation with finite blocklength.To begin with, we present the system model and formulate the analysis of outage probability for OTFS with finite blocklength as an equivalent problem of calculating the outage probability with finite blocklength over parallel additive white Gaussian noise (AWGN) channels.Subsequently, we apply the equivalent noise approach to derive a lower bound on the outage probability of OTFS with finite blocklength under both average power allocation and water-filling power allocation strategies, respectively.Finally, the lower bounds of the outage probability are determined using the Monte-Carlo method for the two power allocation strategies.The impact of the number of resolvable paths and coding rates on the outage probability is analyzed, and the simulation results are compared with the theoretical lower bounds.
Evaluating Machine Learning-Driven Intrusion Detection Systems in IoT: Performance and Energy Consumption
Venue: arXiv cs.NI 2025
Year: 2025

In the evolving landscape of the Internet of Things (IoT), Machine Learning (ML)-based Intrusion Detection Systems (IDS) represent a significant advancement, especially when integrated with Software-Defined Networking (SDN). These systems play a critical role in enhancing security infrastructure within resource-constrained IoT systems. Despite their growing adoption, limited research has explored the impact of ML-based IDS on key performance metrics, such as CPU load, CPU usage, and energy consumption, particularly under real-time cyber threats. This study bridges that gap through an empirical evaluation of cutting-edge ML-based IDSs deployed at the edge of IoT networks under both benign and attack scenarios. Additionally, we investigate how SDN's centralized control and dynamic resource management influence IDS performance. Our experimental framework compares traditional ML-based IDS with deep learning (DL)-based counterparts, both with and without SDN integration. Results reveal that edge-deployed ML-based IDSs significantly impact system performance during cyber threats, with marked increases in resource consumption. SDN integration further influences these outcomes, emphasizing the need for optimized architectural design. Statistical analysis using ANOVA confirms the significance of our findings. This research provides critical insights into the performance and trade-offs of deploying ML-based IDSs in edge-based IoT systems.
A Two-Stage Interpretable Matching Framework for Causal Inference
Venue: arXiv cs.AI 2025
Year: 2025

Matching in causal inference from observational data aims to construct treatment and control groups with similar distributions of covariates, thereby reducing confounding and ensuring an unbiased estimation of treatment effects. This matched sample closely mimics a randomized controlled trial (RCT), thus improving the quality of causal estimates. We introduce a novel Two-stage Interpretable Matching (TIM) framework for transparent and interpretable covariate matching. In the first stage, we perform exact matching across all available covariates. For treatment and control units without an exact match in the first stage, we proceed to the second stage. Here, we iteratively refine the matching process by removing the least significant confounder in each iteration and attempting exact matching on the remaining covariates. We learn a distance metric for the dropped covariates to quantify closeness to the treatment unit(s) within the corresponding strata. We used these high- quality matches to estimate the conditional average treatment effects (CATEs). To validate TIM, we conducted experiments on synthetic datasets with varying association structures and correlations. We assessed its performance by measuring bias in CATE estimation and evaluating multivariate overlap between treatment and control groups before and after matching. Additionally, we apply TIM to a real-world healthcare dataset from the Centers for Disease Control and Prevention (CDC) to estimate the causal effect of high cholesterol on diabetes. Our results demonstrate that TIM improves CATE estimates, increases multivariate overlap, and scales effectively to high-dimensional data, making it a robust tool for causal inference in observational data.